Mass Effect: The Crucible Effect
by cthulu1
Summary: When Shepard refuses the Catalyst's options, having found them to be monstrous, and instead attempts to sabotage the Crucible, it instead fires and the dark energy creates a space/time distortion that sends her into the past. From there she uses her knowledge to fight the reapers and fix the mistakes she made the first time through.
1. Chapter 1

When the catalyst finally shut up, Sarah Shepard walked towards the panels to control the reapers, and shot them. When she sat down and closed her eyes, she saw Miranda smiling while they looked at Oriana after killing captain Enyala. It then turned to the look of terror in her face as she fell to her death, her arm slipping through Shepard's fingers. A few moments later, she was hit by a wave of dark energy, and woke up in the thorian's lair. Liara asked, "Shepard are you ok?"

"I'm fine, Liara." Shepard replied, before turning to Shiala and saying, "Thanks, we need to leave now though." Back on the Normandy, Sarah learned that sure enough, all that was left before heading to Ilos was Virmire. She sighed, at least last time around she'd been able to go kill some cerberus agents. She smiled when she thought about how they'd already handled EDI on the moon. Back in her quarters, she was surprised to see Kaidan, who said, "Commander, what's going on? You've been acting really weird. Ever since you got the cipher you've been completely ignoring everyone. Normally you talk to everyone for hours on end, now you just head right to your quarters."

"That's none of your business, Lieutenant." Shepard growled.

"If it's something that'll affect the mission, as your second in command it's my job to make sure that you're in good enough shape to do your job."

"I'm fine, Alenko. Now get out of my quarters now, if you don't want to be forcefully thrown from the room."

Kaidan glared at her and said, "I'd like to see you try." while flaring his biotics. Shepard grinned and charged him, he managed to hit her with a stasis, and she struggled against it, without any success. He smugly said, "That's what you get for trying to beat the shit out of me, _Commander._" Shepard didn't reply, but instead swore under her breath. When Kaidan left, she said, "Stupid. Still thinking as if I have the upgrades Miri gave me." Then, Liara walked in and asked, "Sarah, what's wrong?"

"Go away, Liara. I'm not in the mood to listen to you ramble." Shepard growled. Liara asked, "What's gotten into you? You've never been like this before."

"Right. I'm not in the mood to speak to you Doctor, so please, leave me alone." Shepard said.

"Fine, Sarah. But I think the cipher may have affected your head." Liara said. Next, Chakwas walked in, and said, "Sarah, why did you chase Liara away? You broke the poor girl into tears."

"You too, Chakwas? If only you remembered." Shepard whispered. Chakwas caught it and asked, "What are you talking about?"

"Nothing, Karin. How are things in medical?"

"They're fine, but what's gotten into you?"

"Nothing. I'm fine, Karin. I'm just really tired." Shepard said.

"Alright, maybe you'll be better after getting some rest."

* * *

Three hours later.

Shepard walked into the shuttle bay, and had Wrex and Garrus go with her to the surface of Virmire. After fighting their way through to the STG team and having a chat with Kirrahe, Shepard talked Wrex down, and told Ashley to go with Kirrahe's men. Shepard, Tali, and Garrus went in behind as Shadow team, and when they found the indoctrinated salarians, Tali said, "We should let them out."

"They're indoctrinated, willing puppets of Sovereign. They'll do whatever it tells them to. It could even take direct control of them. We need to get moving and they'll just delay us." Shepard replied.

"How can you be so certain?" Garrus inquired.

Shepard blurted out, "They did it last time when I let them out."

"What?" Garrus and Tali asked.

"Shit!" Shepard said, "Do not _ever _mention this."

"Mention what?" Garrus asked, "The fact that you're completely insane?"

"You would be too if you'd seen what I have." Shepard replied.

"What the hell are you talking about?" Garrus asked.

"That's classified." Shepard replied.

"What the hell could you have done that is that classified?" Tali asked. Shepard smirked, and said, "One day you'll find out." Garrus didn't accept this, and said, "If you don't tell me what the hell is going on with you, then I'll put this knife into your knee."

"If I told you what it was, you wouldn't believe me." Shepard said.

"Give me a damn answer, Shepard!"

"You don't want to know the truth, Vakarian. If I heard it, I wouldn't believe it if I hadn't experienced it myself."

"Such as?" Garrus asked.

"Me destroying a mass relay, among other things." Shepard said. This made Garrus drop his knife, and say, "What the fuck? Why would you destroy a mass relay?"

"It was that or have us all certainly die." Shepard said.

"What threat could make it necessary to destroy a relay?" Tali asked.

"You'll see in a few minutes." Shepard said. When they had fought their way through to Rana Thanoptis' location, Shepard said, "In the next room you'll see what threat could be dangerous enough to merit the destruction of a mass relay." After using the second beacon, she walked up to where Sovereign said, "You are not Saren."

"Hey Nazara, how you doing? You harvest any civilizations lately? Oh wait, you can't because your pals can't get into the galaxy."

"How do you know of this?"

"I had a little chat with good old Harby before he tried to kill me a while back."

"How do you know of Harbinger?" Sovereign asked.

"Stopped a plan of his. Trying to make a human reaper. Had to blow up a base of yours. Wonder what your little spidery buddies are going to do? Look for the leviathans? 'Cause I can tell you that's a waste of time."

"We are each a nation, independent of all weakness."

"Right, want to go on about how we are insignificant compared to you? Or perhaps how when you come your numbers will darken the skies over every world?" Shepard asked. Sovereign was clearly confused, and when Shepard added, "Or maybe you'll go on about how we can't understand your motivations are not something we can comprehend?"

"This communication is over." Nazara said, before leaving. Garrus said, "You handled that well. What was that thing?"

"Nazara." Shepard said.

"That doesn't explain anything. What are Nazara and Harbinger?"

"Reapers. Ships that harvest organic life every fifty thousand years. The destroyed the protheans a long ass time ago, and they're planning to take us out. If I hadn't detonated that relay, they would have had a back door into our galaxy. Now we need to get going." Shepard said. She moved on, and after killing a few krogan and geth, she chose to rescue Ashley instead of Kaidan, because of how he'd acted towards her on Horizon. And she took note that Saren didn't come to fight like he had before. After that op, and the following discussion with the council, Shepard walked over to Ashley, and said, "He didn't die because of you. He died because he was the best one to detonate the bomb." Ashley nodded, and headed to her quarters. Liara walked up to Shepard, and asked, "Sarah, are you alright?"

"That is none of your business, Doctor T'soni."

"That's it, Sarah. What the hell has gotten into you? Before Feros you were flirtatious, but now you're cold and distant."

"I've been through a lot of shit since then. So, whatever you think I was before I got the cipher, I'm probably not. It subjugated me to experiencing the entire history of the prothean race. It isn't very easy to stay the same after you've experienced that." Shepard said, before settling down in the airlock until they landed on the Citadel. The Council once again ignored her, but she wasn't surprised. After that, Shepard collapsed into her bed, and was surprised when T'soni actually left her alone. Then, Joker said that they'd arrived on Ilos. After landing on the planet, Shepard quickly guided Garrus and Tali through to where they managed to open the doors to the Conduit. Therein, they met Vigil, and Shepard said, "Hey, Vigil. Good to see you're still running. We don't really have much time, so can you just give us the cliff notes on the information on the reapers?"

"Of course. Interesting to see the effects of the Crucible Project. Reapers are ancient alien spaceships that destroy all organic life every fifty-thousand years. The Citadel's secretly a giant mass relay, the Conduit is a prototype mass relay that leads to the Citadel, and a few of the prothean people used it to gain access alter the signal the Citadel gave the keepers so they didn't open up the relay. And here's a program to gain complete control of the Citadel's systems." Vigil replied. Shepard nodded, and walked back to the mako. In the vehicle, the drove towards the Conduit, and it was almost completely torn apart by the attacking colossi before they went through the Conduit. After a few harrowing moments of moving through the mass free space, and then it crashed into several geth units on the presidium. Shepard stepped out of the mako and killed the two other geth. She continued moving through the presidium, and soon they were walking towards Sovereign, but were blocked by a geth drop ship. Shepard quickly began hacking into the turrets, and Garrus and Tali fired on the geth units that dropped down. After hacking the first turret, Shepard sprinted towards the second turret, but was sent flying into a wall by a geth devastator. When she hit the wall, she collapsed to the ground. Before she blacked out, and was back on the Collector Base, watching Miranda slide to her death while Mordin shot at the Collectors from a different platform. When Miranda slipped out of her hands, Shepard was brought to by Garrus, who said, "Shepard, we've got to hurry!" She nodded, and began sprinting to the Citadel Tower. Therein, she killed Saren's two geth guards, and said, "Saren, what the hell are you doing?"

"Ah, Commander Shepard. I was wondering when you were going to arrive." the turian replied.

"I wouldn't want to show up late, Saren. Or early." Shepard said with a smirk, "Why don't you put the gun down and walk the hell away from that panel?"

Saren didn't reply, and Shepard continued, "Can't you see that Sovereign's controlling you? You were a Spectre, one of the best. You were a bit harsh, but you still got the job done. Now you're undoing everything you worked for before, the preservation of galactic peace. You're a willing slave of the reapers."

"You're wrong, Shepard. We can prove that we're useful to them!" Saren said.

"No, we can't. They are harvesting us, to protect us! Their master himself, the little bitch that he is, said that the reapers harvest all organic life in the galaxy to preserve it. Removing the old life to make room for the younger life. Just like they left us behind while they harvested the protheans."

"And yet you still insist on fighting them when you know you can't win." Saren said.

"Maybe, but I'll fight them as many times as I have to. If I have to fight them a hundred times to find a weakness that I can exploit to win, then I'll do it. But ask yourself this, Saren, why the hell are you fighting? Is it for the preservation of your people, or a desperate attempt to save your own ass?"

Saren was shocked, and said, "What right do you have to defend your actions, Shepard? You left your squad to die on Akuze, and your family on Mindoir."

"Yes, but I didn't turn against what they stood for. I didn't betray them to help a group of ships that would murder them. And I've fought the bastards who caused their deaths. I've fought and literally died to protect society from the reapers, but you refuse to even listen. Did Sovereign give you some upgrades?" This got the reaction from Saren that Shepard had hoped for. A look of pure shock crossed the turian's face. She said, "It's controlling you through your implants. You're its puppet, but you can break free, if you've got the balls."

Saren said, "No, I'm not Indoctrinated, Sovereign needs me at my best, so my mind is still my own."

"No it isn't. Sovereign's controlling you, and you don't even recognize it. You're attacking the Citadel, and you're not stupid enough to do that unless you were under something's control." Saren took a moment to think about what Shepard said, and was surprised when he found himself agreeing with the human commander. He said, "It may be too late for me, Shepard." Before putting his pistol to his head and pulling the trigger. It flew through his head, shattering his skull and leaving a massive hole in his brain. He collapsed down into the lower area, and Shepard said, "Time to get this finished." while she activated the program Vigil had given her. A few minutes later she had opened the mass relay and the Destiny Ascension had been rescued. Then Saren was animated by Sovereign through his implants. She calmly dodged his attacks, and fired a round into his head, causing him to stagger backwards, where Garrus and Tali were waiting, grabbing the possessed corpse. She put her assault rifle to its head, and fired until it overheated, where she tried to pop out the thermal clip, which only resulted in her hand getting hit with steam, and Tali and Garrus laughing at her. She glared at them and was soon hit by some flying debris. A day later, she staggered out of the rubble. A few weeks later, she was sent to the Terminus Systems and there the Collectors struck again. When Shepard felt the air leaving her suit, she just smiled, knowing what she would wake up to.

* * *

**A\N: So, to those of you who read Meus Mundus I haven't quit writing it, but every time I tried to write it, I kept writing it basically like this one. There'll be more chapters, but they may be sporadic in coming. Thanks for reading and please review. **


	2. Chapter 2

**A\N: Shepard was just rushing through ME1 in the last chapter and Cerberus wouldn't really know about how Shepard was acting. As to some of the other weird actions like why she wasn't excited to see her crew will come out later. (Partially because only one of them had died.) And to the person who said it was just another convenient time travel story, I read several of them before I published this, and they weren't so much of a time travel story as they were putting Shepard A into Shepard B's body and universe after Eden Prime. And in the codex it says that dark energy weapons create space time distortions, and the crucible works as a giant one of those. It would be perfectly possible that the activation of something that uses that much dark energy would cause a massive time distortion that sent Shepard back in time, because she was at the heart of the blast.**

* * *

Lazarus Station.

Miranda walked towards the room where Shepard was being kept, and inside Wilson said, "Miranda, we're sixty percent done. Shepard should be back among the living again in approximately two months time."

"Good. How are the cybernetic implants working?" Miranda asked.

"They're working at 110% of what we expected. Shepard will be even more of a force to be reckoned with than she was before she died."

"Good, we need to start working on Shepard's brain now that it won't die on us if it's left alone."

* * *

Lazarus Station one month later.

Shepard opened her eyes, and saw Miranda yelling at Wilson. She smiled at the Cerberus Operative, and tried to grab her arm, but Miranda noticed this and gently put Shepard's arm back on the side of the bed. Shepard tried to warn her about Wilson, but the words didn't form. Miranda was shocked by the Commander's actions. When she'd turned to look at Shepard there had been a huge idiotic grin on the Commander's face. She sighed and headed back to her quarters. While walking there, she wondered what was wrong with Shepard. They'd never met, yet the Commander seemed ecstatic to see her. She collapsed into her bed and quickly fell asleep.

* * *

Lazarus Station, two weeks later.

The station was rocked by an explosion, and Shepard was knocked awake by it. Over the loudspeaker Miranda said, "Commander, get out of that bed now."

"Sure, Miri. How are you?" Shepard asked.

"Now isn't the time for idle conversation, Shepard."

"Right." Shepard said while she pulled on her armor, and grabbed the pistol, and Miranda was surprised because there was no way Shepard could have known they were there. "How did you know to find your armor in there?"

"Well, when I was hunting Saren the people I went after on side missions always kept equipment in lockers like that. It was really weird." Shepard said while she took cover before the door exploded. She then sprinted forward and grabbed the thermal clips on the ground and popped one into her pistol. She then activated disruptor rounds and shot the three mechs that came in through the door. She then sprinted to the next area where she grabbed the grenade launcher and used it to kill the mechs that came through. She then took the lift down and sprinted through the fire. In the next area, Miranda said, "Get to our head of security Jacob Taylor. He'll guide you to the shuttle bay."

Shepard said, "Well, so far things are going normally." before she met up with Jacob and killed the mechs in the room. She said, "Taylor, we need to go. Wilson needs to have his ass kicked." before walking off followed by Jacob who was confused by Shepard's actions. Inside server room B, Shepard shot Wilson in the head, and continued through the station. She shot a group of mechs heads off before heading to the shuttle bay. Inside, Miranda was standing and said, "Where's Wilson?"

"Dead." Shepard said.

"That's good. Did you find any survivors?"

"No, everyone else is dead. I'm sorry, Miranda." Shepard said.

"There was nothing you could do. Wilson had sabotaged the security systems before you were up and on your feet." Miranda replied. In the shuttle, Miranda asked Shepard the same questions she had before the first time. Afterwords, Shepard asked, "So, Miranda, what do you know about TIM."

"Not very much. His file's incredibly well protected."

"Well, I'm sure that TIM is pleased with it. However, I had a few friends find what they could on him. His actual name is Jack Harper, his eyes were messed up by reaper tech, and he's completely insane. He honestly thinks that the best way to handle the reapers is to try and control them. Which, while theoretically possible, would require some sort of organic AI interface. And that kind of technology could have any number of unforeseen negative consequences." Shepard said.

"Who are your contacts?" Miranda asked.

"They aren't alive anymore. Died a while ago." Shepard said.

"That's unfortunate. I'd be interested to learn more the Illusive Man. But how do you know we work for Cerberus?"

"You had the Cerberus emblem everywhere."

Miranda nodded and said, "You have a good point there."

"Yeah," Jacob said, "what are you planning to do when you see the boss?"

"Give him a piece of my mind. The bastard made a few mistakes last time I had to deal with Cerberus. Maybe he'll even tell me where to find that bastard Kai Leng."

"What? You've never encountered Kai Leng before." Miranda said.

"Forget it." Shepard said.

"What do you have against someone you don't even know?"

"Not all of my encounters are open, even to Cerberus." Shepard growled.

"Of course, Commander." Miranda coldly replied.

* * *

Cerberus Cronos Station.

The Illusive Man turned his chair around when Shepard showed up in the QEC. "Commander Shepard." he said.

"Jack Harper." She replied, to his surprise. "Surprised that I know your name?"

"It isn't that important." TIM replied.

"Right, what do you want?"

"Human colonies are disappearing. I think the reapers are behind it."

"Why bring me back?"

"You've not just talked to a reaper, but killed one. You know them best, Shepard."

"Right, what else do you want, Jack?"

"Nothing. I just want you to help us end the attacks."

"Why should I trust you?" Shepard asked.

"We brought you back to life, Shepard. If it wasn't for me, you'd be dead."

"From what I understand you just funded the project. Lazarus was handled by Miranda."

"And if she'd had complete control over it, you'd have a control chip in your brain."

"Care to tell me something I hadn't already been able to figure out or found out about through the multitude of terminals that were left lying around on the Lazarus station?" Shepard asked. TIM was surprised, but said, "The latest colony to be hit was Freedom's Progress. If you find enough evidence to prove that it's something that you think you should look into, then fine. But if not, then we cut all ties." TIM said.

"Right, I'll look into it. If I find enough evidence I'll work with you." Shepard said as she walked away. In the next area, Shepard said "Ms. Lawson."

"Commander." Miranda said.

"Tell me a bit about yourself, Miranda." Shepard said.

"We don't really have time for that, Commander."

"If I'm going to work with you, Miranda, I'm going to need to know you." Shepard said.

Miranda sighed, and said, "I can crush a mech with my biotics, or shoot it in the head from over a hundred meters."

"I didn't want a resume, Miranda. I wanted to get to know you as a person."

"I'm not looking for a friend, Shepard."

Shepard said, "Miranda, relax. I'm not going to try and manipulate you."

Miranda was surprised, and said, "Well, then you should know that I've had extensive genetic modification. Not my choice but I make the most of it. I'll probably live a time and a half as long as the average human and my biotic abilities are quite advanced, for a human. Everything about me was designed to be perfect. My biotics, my early training, even my looks were designed to give me an edge."

"It's hard, isn't it? Feeling like everyone expects you to be perfect."

"What would you know about it, Shepard?" Miranda asked.

"Ever since Akuze, the Alliance expected that I do everything perfectly just because I'd managed to escape the threshers and then killed them. Every last time I screwed up, it felt like the Alliance brass were angry with me." Miranda nodded, and returned to her work. Shepard walked over to Jacob and said, "Hey, Taylor."

"Commander, I'm glad that the Illusive Man talked you into working with us." Jacob replied.

"I don't trust Cerberus. I never will. I'm just doing what I can to help those colonists."

"Fair enough. Do you trust me, Commander?"

"You're a good man, Jacob. But you're working for the wrong people."

"I thought the same when I was with the Alliance."

Shepard laughed, and said, "The Alliance isn't as bad as it might seem. All that red tape keeps the people in line."

"Even in the Corsairs there was enough red tape to sink a cruiser." Jacob said, and Shepard just nodded. In the shuttle to Freedom's Progress, Shepard began working on a plan for when they attacked the Collector base. Quickly reconstructing the map of the structure EDI had provided, Shepard began working on it. Both Jacob and Miranda were in the passenger bay while Shepard was in the cockpit.

* * *

In the passenger bay, Miranda said, "I think Shepard's different somehow. She has behaved completely different from what the reports on her suggested. She hasn't been particularly hostile, but she also doesn't trust Cerberus. Do you think I could have screwed something up in the reconstruction?"

"Miranda, Shepard's fine. I'm sure that the data we had gathered just didn't mention how she would behave." Jacob said, while the shuttle landed, and Shepard came back into the passenger area. She pulled out her avenger, mumbled something about a typhoon, and then continued moving through the colony, ignoring the comments Miranda and Jacob made. When they found Tali, the quarian said, "Shepard? Is that you?"

"The one and only." Shepard replied with a grin.

"Prove it's you. What did you call Sovereign on Virmire?"

"Name or what it is?"

"A name, Shepard."

"Nazara." She replied.

"Wait, you're saying that Sovereign called itself Nazara? Why would it have a name in old Turkish?" Miranda asked.

"What the hell are you talking about, Miranda?" Shepard asked.

"Nazara is old Turkish for one who observes, or one who sees. Why would Sovereign have a name for itself in an earth language?"

"Probably just a translation from the actual name." Shepard said. Tali was satisfied with Shepard's information and agreed to help them. When they reached the heavy mech, Shepard said, "Miranda, hit that thing with an overload. Jacob, give us a barrier so it doesn't tear through our shields."

The Cerberus operatives complied, and when the mech's shields collapsed, Shepard fired two grenades into it. When the mech exploded Shepard grinned and headed straight to Veetor's location. After a brief chat and recovering the info on the Collectors attacking, Shepard took Miranda and Jacob back to the shuttle and left Veetor with Tali.

* * *

After her second conversation with TIM, and getting the new Normandy, Shepard set course for Jack's location, hoping to be able to make the convict not try to kill Miranda. She then headed to Miranda's quarters, and asked, "How are you doing, Miranda?"

"I'm fine, Commander. The mission to Freedom's Progress went extremely well."

"We lost four of the quarians, that isn't exactly what I'd call a stunning success."

"They disobeyed their orders and moved in too early. It isn't our fault that they died." Miranda said.

"Yeah, but I still feel bad about it. That was one of Tali's first command roles, and everyone else ended up dead."

"What makes you say that was one of her first command roles?"

"The way the team treated her. She obviously hadn't proven herself to be a leader in the eyes of that team. I've learned how to catch onto these details."

"Of course, was their something you wanted to talk about, Shepard?"

"Miranda, please, call me Sarah."

"Um, okay. Sarah, was their something you wanted to talk about?"

"Earlier you said that your genetic modification wasn't your choice. Who forced you to be modified?"

"My father did. He's an incredibly wealthy man, and he wanted to create a dynasty."

"What about your mother? What did she think of his plans for you?"

"I don't have a mother. I was made in a test tube. My father took his own DNA and his Y chromosome was changed with desirable traits from multiple sources."

"So, your father was a cold man, wasn't he. Raised you with unreasonable expectations, and eventually you got fed up and left?" Shepard asked.

"Correct. I didn't think I'd been that obvious about it."

"It's the only logical explanation. If you'd stayed with him you'd have had a life of wealth and luxury. Except he didn't treat you like a person. You were just a tool to him. But, that isn't everything." Shepard said, thinking of the Shadow Broker's files on Miranda.

"What tells you that?"

"You act as if all you are responsible for are your mistakes. You were made to be perfect, but you obviously think that you are far from it. And it isn't just something to do with how you've taken your life. Something more basic. It's all in your demeanor."

"The files didn't mention you were this good at reading people."

"They didn't because I didn't want them to. I made sure that no one put that detail in. It gave me an advantage." Shepard said.

Miranda nodded, and said, "You're not what I expected."

"I've heard that a lot. I've seen a lot, so I don't seem like what most people would expect a hero to be." Shepard replied, her eyes filling with tears.

"Sarah, are you all right?" Miranda asked.

"Just thinking about something."

"What?"

"Sorry, Miranda, this is something I wouldn't tell anyone. It's private. No one will ever know what it is."

"Not even Doctor T'soni? Your old lover."

"T'soni and I didn't become lovers. She wanted it, but I made it clear that I wasn't interested." Shepard said before walking out, hoping that Miranda would remember the night before they'd gone to the derelict reaper.

* * *

Shepard stood on the balcony in the turian councilor's mansion. She stared out into space, and Miranda walked up. The Cerberus agent said, "Sarah."

"Miri." Shepard replied.

"It's a beautiful view."

Shepard looked Miranda in the eye and said, "Not as beautiful as you, Miri."

Miranda looked uncomfortable, but Shepard continued, "Miranda, you're one of the best people I've ever met. You may work for a group that I despise, but you're doing it for the right reasons. You have a firm belief of what is right and wrong, and you let everyone know when you think they're doing the wrong thing. You always act like an ice queen, but you do so to protect yourself. The only time I've seen the real you are when I first woke up on that bed on Lazarus Station, and when you went and talked to your sister. I know you may not be comfortable with this, but I care for you Miranda. And I think you care for me."

"Yes, but now isn't the time for emotional entanglement. There's the mission at hand, and then the reapers. We could all be dead in a few days."

"If we're all going to die, I'd rather die with you at my side than alone."

"I thought you'd rather get back to T'soni."

"Liara and I were over before the Normandy was destroyed." Shepard replied, and Miranda was surprised. The Commander placed a hand on Miranda's shoulder, and gently kissed her. A few moments later, Miranda said, "Maybe you're right. So you better promise me that you won't die on me."

"I promise. We'll both see the end of this war with the reapers." Shepard said, holding Miranda close.

* * *

Shepard stared into space from her bed in the loft, when Chambers walked in and said, "Commander, Joker wishes to speak to you."

"Why didn't he have EDI tell me?" Shepard asked.

"Mr. Moreau doesn't trust me." EDI said, which caused Shepard to nearly fall over she laughed so hard. Both Chambers and EDI were confused, and Shepard was clearly not going to be able to explain. Or willing. When Shepard had finally quit laughing she asked Kelly, "What's your name?"

"I'm Yeoman Kelly Chambers."

"Kelly, thanks. EDI thanks for the laugh." Shepard said, before going to talk to Joker.


	3. Chapter 3

Prison Ship Purgatory.

When Shepard, Miranda, and Jacob walked into the entrance area, the guards said, "Give up your weapons immediately."

Miranda and Jacob looked to Shepard, who said, "We aren't giving you our guns."

The guard said, "Then I'm afraid I cannot allow you to enter this facility."

Shepard calmly aimed her pistol at the guard and was about to pull the trigger when Warden Kuril said, "Commander Shepard, please relinquish your weapons. This is a high security facility, and we don't want to risk any escapes."

"Listen, Kuril, I am not letting go of my weaponry. If you expect me or anyone in my crew to do as you say then you can be the first to get a bullet between the eyes."

Kuril looked at Shepard and realized she was serious. '_She's too valuable to risk not getting her. She'd make me billions of credits._' "Very well, three armed visitors won't cause a mass breakout."

'_That's what you think, bastard._' Shepard thought, while the turian droned on about how well secured the ship was. When he'd walked away talking about checking if the funds had cleared and told them to go check the clearing area for Jack. Shepard nodded, and pulled out her assault rifle. She motioned for Miranda and Jacob to pull out their weapons. After Kuril revealed his treachery, Shepard and co fought their way back to the corridor. There, Shepard said, "Miranda, head to the Normandy and have Joker pull out of here. When we've taken care of Kuril and recovered Jack we'll signal for the Normandy to pick us up. You may want to have him destroy the engines of this ship so that they don't escape using FTL."

"Of course, Commander." Miranda said while she walked off.

"Okay, what the hell was that about?" Jacob asked.

"What are you talking about, Taylor? I needed to ensure that the Normandy wasn't in danger of being destroyed."

"Riiiight." Jacob said, "And that was the same reason you seemed to not want to do it... As if you didn't want to, but your plan required it."

"What are you trying to say, Taylor?"

"You may not have noticed, but you always stare at her when she isn't looking, and you think no one else is. Also, you keep glancing at her to make sure she's ok."

Shepard dismissed it quickly, and released Jack. The biotic destroyed the two mechs and then looked around herself, appearing to be really confused. Shepard walked up to her, and asked, "What's the matter?"

"How the fuck did I end up back here, Shepard?"

"Jacob, go ahead and make sure that there aren't any guards. I need to have a chat with Jack."

"Understood, Commander." Jacob said.

When he was gone, Shepard said, "From what I've been able to figure out, it was a side effect of the Crucible firing. The Catalyst said that it was a giant battery, and that together with the Citadel and the relays it could release enough energy to destroy the reapers. It also said that the Crucible could be used to create a new form of life, that was both organic and synthetic, or to take control of the reapers."

"I thought the Catalyst was the Citadel." Jack said.

"It's actually an idiot AI on the Citadel. It said that it didn't interfere with us before because it couldn't really interface with the Citadel's systems unless the Crucible was attached. It took some persuading, but it did admit that it had designed the Crucible. It planned to use it as a way to finally get its precious synthesis to come about."

"Well, what did you do?"

"I shot the panels it told me would let me take control of the reapers. Then I sat down and waited for the inevitable." Shepard said, before walking towards where Jacob had been. After finishing the mission, and returning to the Normandy, Shepard went to talk to Miranda while Jack went back to her old room. In Miranda's quarters, Shepard asked, "How are you doing, Miranda? You don't look too good. Well, for you, anyways."

"Sorry about that, Commander, I've just been having some strange nightmares. I keep dreaming I'm sliding down to my death. It's really strange."

"Not really, Miranda. We both know that chances are in favor that we won't survive this mission to stop the Collector attacks. You're probably just stressed out over the risks."

"You're right, Commander." Miranda said.

"I seem to remember telling you to call me Sarah." Shepard said with a grin.

"Sorry, Sarah. I've had a lot of stuff on my mind. Where will we be going next?"

"We'll be heading to Omega to pick up Mordin Solus and Garrus." Shepard said.

"Garrus has been missing for a few months. What makes you think he's on Omega."

"Have you read the files on Archangel?" Shepard asked, "He's a turian who primarily uses a sniper rifle, and has a habit of saying boom headshot. Garrus is the only turian in the galaxy who uses that line."

Miranda nodded, and said, "That would be a reasonable way to say that he is Vakarian. It is possible that he is just emulating Garrus to get more of a reputation."

"I suppose that's possible. But, if he was doing that, then I'm sure Garrus would hunt him down and kill him. He doesn't like people who imitate him."

"Not surprising. Is there anything else you'd like to talk about, Sarah? I've got a lot of work to do right now."

"If that's the case, I'll let you go." Shepard said, before walking out and asking Kelly, "There anything I need to know about, Kelly?"

"You have several unread messages at your private terminal."

Shepard nodded, and started reading through the messages. In the list, there was a single message from Liara. This confused Shepard, because before there hadn't been a message from the asari before Horizon. She pulled it up, and discovered that it was actually from a certain individual who would like to see her on Omega. This certain individual said that he was a batarian with a personal grievance against Shepard. She sighed, and replied, "Whatever your personal problems are, I do not have the time to fight you. Perhaps in a few months time I will be able to engage you in combat. Until then, deal with it." She then went to Jack's quarters, where she asked, "What are you doing, Jack?"

"Making sure TIM isn't watching. That way we can talk without him listening in." the ex-con replied.

"And?"

"There were 17 security cameras in this room alone. I had to destroy them, then there were several microphones, that I put in the men's room toilets. Let's just say that he'll have a very... unpleasant sound to listen to every time he checks in on this room."

"Good, what do you want to talk about?"

"Well, for starters, what the fuck do you plan to do? We know everything that's going to happen, which means we can fucking change history however we see fit."

"Not really. There are certain ways we can't change it. We weren't sent far enough back to prevent the creation of the reapers. So, we can fix our mistakes from here on out. And Jack, don't attack Miri."

"Don't worry, Shepard. I don't want to turn you against me. And, you'd probably literally bite my head off if I hurt her." Jack said.

"Probably. I was thinking that we should take a few more precautions when we fight the Collectors. I've already started working on a plan for when we attack the base. Made a map of the base and the space around it and where we were attacked by the Collectors' defenses. That way we can be better prepared."

"Well, you can't tell anyone about how you know this shit. So what could you do to prevent the attacks? And what about when we get trapped on the Collector ship? That was a pretty dangerous op."

"First off, we'll both be going, that way when we get attacked, we'll be safer. Since we know what the Collectors will send after us we'll be able to handle their attacks more easily." Shepard said.

"And what about the base where the cheerleader dies?"

"She won't be going on that mission. I'll arrange a situation with her sister, or have her put into a coma before we go through the relay."

"You may want to rethink that, Shepard. The Cheerleader's not someone who would like being put into a coma just to keep her safe. Just leave her to help hold the door. That way she won't fall off the platform. " Jack suggested.

Shepard replied, "You're right. Well, here's a copy of the map I made. Let me know if there's anything else you need."

"You never told us what really happened to Mordin. He went up to cure the genophage, and didn't come down. I never cared too much for the salarian, but it doesn't make sense what would cause him to not make it back out of there."

"The Shroud had been tampered with. He had to go up to make sure that the cure would be viable. The shroud collapsed before he could get down." Shepard said as she walked back to the loft. Therein, she saw that there was a picture of Liara. She quickly grabbed it and cracked it over her knee. She then collapsed into her bed, rapidly falling asleep.

Five hours later, Joker said, "We've arrived at Omega. You may want to start working on recruiting the specialists."

"Right." Shepard said, before exiting the loft and telling Miranda and Jack to meet her in the airlock.

* * *

**A\N: Sorry this chapter is really short, but I noticed that what I had planned for this chapter wouldn't really fit for how early in the story it is. Thanks for reading, and please leave constructive criticism in the form of a review. Next Chapter will probably be longer in coming because I've been feeling more into Meus Mundus than this since last chapter.**


	4. Chapter 4

**A\N: So, I skipped most of the first recruitment missions because I found them boring to write.**

* * *

Horizon.

Shepard walked up to where the Collectors had taken several of the colonists, and said, "Damn! We're too late to help them."

"Yeah, the Normandy wouldn't be able to last in a fight with that ship. Our cannons and armor might be better, but our kinetic barriers wouldn't be able to hold up against their attacks." Garrus said.

"Right, we'll have to move quickly to prevent them from getting any more colonists." Shepard said, and began sprinting through the area, firing on Collectors with her Mattock, pulling the trigger so fast that it was almost firing fully automatic.

Miranda fired her Carnifex into a Collector's head, and Garrus fired his vindicator at a scion. The sac on its back burst, and the massive husk stumbled right into Shepard's shotgun, which she fired and blew the thing's torso out. It fell dead, and Shepard then leaped at another Collector, who she stabbed in the head with her omniblade. It fell down, and she stabbed the Collector Captain near her in the torso with the gleaming blade. She then pulled out her pistol and put a single round in the head.

A Collector charged, and tried to stab her with its extending blades. She ducked below its attack, and kicked it into a wall. She fired a single round from her shotgun into a charging abomination, and then fired a round from her pistol into the Collector she had kicked. With all of the Collectors nearby dead, she went back to where the Collector Particle Beam was and picked it up. They then encountered the crazy mechanic, who Shepard just punched, knocking the poor guy out.

In the middle of the colony, they got to work on connecting EDI to the Gardian towers. When they had hooked the AI up to the towers, they set up on the patio of a nearby building. As Collectors husks and abominations charged, the team opened fire with all of their weapons, only Shepard didn't use the Particle Beam. After a while, a Praetorian arrived, and Shepard pulled out the alien weapon. She fired it on the praetorian until it brought up its barriers. Shepard waited for it to go down, but Miranda tried to get through it with her biotics, only to be grabbed by the praetorian. Shepard swore, and fired a few grenade launcher rounds into the praetorian.

The machine dropped Miranda, and turned to Shepard, who dropped the grenade launcher and fired the particle beam right into the enemy. After a few seconds it hit the mech's more vulnerable underside. The beam went clear through the mech, and it collapsed to the ground, right on top of Shepard.

Garrus ran over to Shepard and tried to move it, but it wouldn't budge. He kept pulling on it, and when Ashley walked up, she asked, "What are you doing?"

"Shepard's under this damn mech!" the turian replied, panic clear in his voice. Ashley started helping, until Miranda lifted the thing with her biotics. Shepard gasped and said, "Thanks, Miranda. Thought that thing was going to stay on top of me for a few more hours."

Miranda replied, "I was just doing my job, Commander."

Shepard shook her head, and turned to Ashley, she said, "Williams."

"Shepard, why the fuck are you working for Cerberus?" Ashley asked.

"I'm not working for them. I'm taking advantage of their resources until I have enough free time to destroy the organisation. When the Collectors are gone, I'm going to turn my attention to Cerberus."

"We can't trust you. You're just a puppet of Cerberus for all we know."

"You're being a damn idiot, Williams! If I was a puppet of Cerberus I'd be trying to recruit you to Cerberus, and I probably wouldn't even look normal. Implanted with reaper tech, so I look like a fucking husk."

"The Illusive Man wouldn't do that." Miranda said.

"You'd be surprised at what he'd be willing to do to maintain control over his people. Miranda, did you ever hear about Praggia?"

"No, what are you talking about?"

"On the planet Praggia there was a project to try to maximize the biotic potential in humans. They tortured the kids, made them fight each other, and whenever they attacked had them doped up. They were willing to do anything, and left false reports about what happened in there. The Illusive Man had them lie on those reports so that he would appear to not have been aware of what was really going on."

"What data do you have that would prove this?" Miranda asked.

Shepard closed her eyes, and was about to reply when the mechanic shot her in the gut, saying, "You betrayed us, Shepard."

She winced, and said, "What the hell are you talking about?"

"You promised that if we assisted you, the reapers would not see the end of the year. Yet, they still live. Your device failed to destroy them!"

"Leviathan." Shepard growled, "What the fuck are you doing. Go back to your precious darkness, and leave us alone. You were completely useless on earth. When Harbinger attacked Hammer on our way to the Conduit, and your left him alone. You didn't try to take him down with your spheres like you did the one on your planet. You let us get decimated, so we couldn't fight back. You didn't help us when we needed it most. Your actions left me injured, broken, bleeding out, while I tried to get to the Conduit. You didn't help. You didn't take down a single reaper on earth. No wonder you got your cuttlefish asses handed to you by your own creations. I bet it didn't even take the reapers a decade to harvest every one of you."

The Leviathan roared, and charged Shepard. She grabbed the possessed mechanic and pinned him to the ground. It said, "We are the first, the apex race. The reapers took over a thousand years to destroy us!"

"Right. And they took a thousand years to conquer earth."

"You lost your world in a single day, it took them a century to take ours!"

"And they built the Citadel? Don't fucking lie to me. The Intelligence, who should be called the Idiocy, is on the Citadel. It hadn't been moved."

Leviathan said, "So be it. Your cycle will end in death for all that you know and love. Including the dark haired operative." before releasing the mechanic.

Shepard's eyes were glowing dark red, and she said, "Just you wait, I'll fucking drop the Citadel on you! The reapers are less annoying than you! All they're trying to do is control or harvest us. But the Leviathans, they try to make you think they're the most powerful race in the galaxy, but all they had going for them was that they didn't have the reapers to come and harvest them before they got more advanced."

Miranda asked, "What the hell was the mechanic babbling about? Humans aren't the first race, and most would say we aren't an apex race"

"It wasn't the mechanic." Shepard replied.

Ashley jogged over to the mechanic, and after a moment said, "What the hell happened to him? He's comatose."

"That's what happens when the Leviathans control someone for hours. When they release them, it can have negative side effects such as comatose. Especially if they're trying to prevent you from talking."

"Who are the Leviathans?" Miranda asked.

"They're the one who's mistakes have affected every civilization since them. They created the reapers, to find a solution to a problem that is something that is more theoretical than factual. Based on an assumption they made after a few events in their time. Then, I give their 'intelligence' valid proof that their problem doesn't exist in our time, and it fucking ignores me!" Shepard said.

"What are you talking about? And what did it mean when it said you love a dark haired operative?" Ashley asked.

"Yes, that was a bit strange."

Shepard said, "I'll explain everything, but not here." before heading into the shuttle, followed by Ashley, Miranda, and Garrus. There, she said, "In about eight months time, the reapers will arrive. They'll take the earth, and I'll have to go and gather alliances. First, I'll go to mars, where T'soni will have found the plans for a device that she thinks will be capable of destroying the reapers. Then, we'll go show it to the council, who will just flat out say they can't help. Then, we'll have to go to Palaven to get help from the Primarch, who we find out is dead. We'll go to the moon Menae, and find out the Primarch is dead. Then, after a while, we'll find out who the next primarch is, and pick him up. Then, we'll have to find a cure for the genophage. Following that, well, we then go to the Citadel which has been attacked by Cerberus. Then, I'll end up helping the quarians and geth resolve their problems. Then, I'll go back to the Citadel, and hear from Tevos, that on Thessia there are a few things which could help us, but things don't go well there. Then, we go to Horizon, where we have to kill Henry. Then, I have to go and attack TIM's base, where he isn't and we find out what the last piece of the puzzle we need to activate the device is. Then, we'll go to earth, and fight the reapers. After a while, we'll go for an energy elevator to the final piece of the device, to prepare it for applying it. Through the elevator, and some corridors, there will be TIM. He'll somehow control both Anderson and myself. And, force me to shoot Anderson before I talk him into putting a round into his head. Then, after a few minutes, I'll be lifted to where some stupid star child says that I have to take one of three idiotic choices. Then, the massive amount of dark energy the device releases somehow sends me back in time to before the reapers arrive."

Ashley said, "That's a load of bullshit!"

Miranda disagreed, saying, "With a sufficient amount of dark energy it would be possible. But, that amount of dark energy would be nearly impossible to produce. But, I would like to ask what the hell the Leviathan meant when it said about loving a dark haired operative."

Shepard shook her head and said, "Figures that the one thing I hoped would be ignored would be asked. Sorry, Miranda, but that isn't going to be one I'm willing to talk about. It's a bit too personal."

"Okay, what about talking about killing my father?"

"After a few events, including your death, your father started working for Cerberus and kidnapped Orianna. When we went to the facility where he was working, we had to kill him to protect Orianna."

"Wait, I died?" Miranda asked.

"Yeah, that did happen." Shepard said, "Sorry about that. Might be a bit... strange to hear that you were dead."

"Yeah," Garrus said, "What about the other stuff. Like, you know, curing the genophage."

"That didn't go as well as I had hoped, we lost a lot of good people. Wrex was grateful, but a lot of other people died who shouldn't have. I made a lot of mistakes before, and I hope that I can fix it this time."

"And resolving the quarians and geth?"

"That took a bit of political maneuvering. I had to make someone make a sacrifice for the good of his people. Then, I had to fight a reaper on foot, just to get the geth to where they would be able to be communicated with. That was the most difficult fight of my life."

"You fought a reaper on foot?"

"Yes, I was using a device to focus the attacks of the entire Migrant Fleet on it."

"That makes a lot more sense than firing regular firearms at a reaper." Garrus said.

Shepard nodded, and headed out of the shuttle since they were back on the Normandy, she also said, "Miranda, don't tell the Illusive Man what I talked about, please. It would be better for everyone if he didn't know."

"Don't worry, Sarah. What you mentioned has me a bit concerned about what direction Cerberus is going."

* * *

**A\N: So, the truth about Shepard has come out. And it may seem a bit early, but it was planned to be on Horizon. I found the mechanic to be a bit weird, so I decided to have him be a victim of the Leviathans, who were affected by the Crucible for a reason that not even they know. It'll just be a mystery. Thanks for reading and please review.**


	5. Chapter 5

Shepard walked up to Kelly, and asked, "There anything I need to know about?"

"Operative Lawson would like to speak with you. As would Professor Solus."

"Got it, is there anything else I need to know about?"

"Not at the moment."

"All right, I'll look into this stuff when I have the time." Shepard replied as she headed to the bridge.

"Hey Commander. Heard about what happened on Horizon. Shame about Ash."

"Yeah, I figured she'd be a bit more forgiving than she was. I saved her life, and she isn't willing to accept that there is something that I have to do because I need resources to fight the reapers."

"Don't worry about it, I'm sure you'll be able to get her to relax."

"Maybe, but I don't have time to deal with her whining about Cerberus. Set course for Illium."

"Got it. And you may want to keep an eye on Jack, we can only hold so much crazy."

"If you were able to keep the ship together with me on board, Jack won't be any problem." Shepard replied with a grin.

-=0=-

Miranda was writing a report, when Shepard walked in. The Commander said, "Hey, Miranda. You wanted to talk to me?"

"Yes, I'm having a bit of trouble with my sister's protection. It looks like my father's found her."

"And you want my help?"

"Yes. I understand that we're busy with the Collector mission. But, if we have the time I'd like to go and make sure that she's safe."

"Where is she?"

"She's on Illium."

"We can handle it easily then. We're already headed to Illium to pick up the Justicar and the Assassin."

"Thank you, Sarah."

"No problem, Miranda. I do what I can for my crew."

"I know, but thank you."

-=0=-

Shepard was in her quarters, reading her email. One stuck out to her. Its contents were this.

Commander Shepard.

We have given you a small gift. One that we believe you will greatly appreciate. It will take time to activate though. It will take some time for it to come into effect, though. There is a small manner we shall discuss after you have passed through the Omega 4 relay and defeated the Collectors.

Sender Unknown

Shepard quickly de-activated her terminal, and asked EDI, "What's the status of the Normandy's weapon systems?"

"They are running at 100%"

"What about the propulsion systems?"

"All systems are running at 100%, Shepard."

"Good. ETA to Illium?"

"Seven hours, Commander."

"Got it. I'm going to get some sleep. Tell the crew that if they need anything it can wait a few hours."

"Is there anything else?"

"Make sure to wake me up in six hours." Shepard replied.

"Understood. Logging you out."

-=0=-

Shepard walked out of her quarters and was greeted by Mordin who said, "Shepard, slight problem. Seeker swarm countermeasure has a small problem. Will not last more than two consecutive hours. With time, and access to palladium and eezo should be able to both strengthen countermeasure for more seekers. Also extend duration."

"You'll get what you need. What did you want to talk to me about?"

"Personal problem. Told you about work on genophage modification project. My assistant, Maelon, has been captured on Tuchanka. Would appreciate if you could help rescue him."

"We'll go to Tuchanka after we finish doing what we need to on Illium."

"Thank you, Shepard." Mordin replied, leaving the loft. Shepard booted up her terminal, and saw a message from Liara. It was just the asari asking for her help with the Shadow Broker op. Shepard laughed to herself, and just left after Mordin.

EDI said, "Commander, we have reached the relay leading to Illium. Illium ETA is thirty-five minutes."

"Good. Tell Miranda and Garrus to get ready to move. We'll have a lot of work to get done when we arrive on Illium."

"Done. Logging you out."

-=0=-

When the Normandy had docked, the ground team exited and were greeted by an asari, who said, "Commander Shepard, all docking fees have been waived."

"Why?"

"Liara T'soni has paid them on your behalf."

"Figures. Am I right in assuming that T'soni wants to talk to me?"

"Yes, and seeing as she paid for you to dock, it would be wise to do so."

"I'll talk to her when I need her help. But I've got some work to do before then." Shepard said, walking away. When they reached Eternity, Shepard said, "Miranda, this is your sister in danger, so you can take point."

"Thanks, Sarah." Miranda replied.

In the private room, Lanteia said, "Miranda, you put a man called Niket as your trusted source. He offered to handle the move himself."

Miranda asked Shepard, "What do you think?"

"It isn't my sister in danger, I can't make the choice for you. It's your call."

"Alright, let him handle it."

"Got it. Also, your father has hired Eclipse to acquire Orianna."

"Thanks for the warning. We'll take care of it." Shepard said.

When they exited, Miranda said, "I never planned on Eclipse, but they never planned on you."

"Strangely enough, no one ever does plan on me."

"Probably because almost the entire galaxy thinks you're dead."

"True."

-=0=-

When the skycar crashed near one of the Eclipse Captains and his team. He said, "So, you're the bitch who stole the boss's little girl."

This pissed Shepard off, and she just shot the guy in the head. The rest of the Eclipse team opened fire on the squad, but Shepard dropped a crate on their heads. The team moved through the area, where Miranda found an Eclipse radio. Captain Enyala said, "Hold off the commandos that are headed this way. We need to give Niket time to move the kid."

"That can't be right. There has to be another explanation. Niket wouldn't."

Shepard placed a hand on Miranda's shoulder, and said, "Don't worry. It'll be alright."

When the elevator had arrived at the next level of the docking area, the team was ambushed by a few Eclipse mercs. Garrus tried to take them out when a hurricane of energy filled the area and tore the mercs limb from limb.

The team looked at each other, until Shepard asked, "Who did that?"

"Wasn't me." Said both Miranda and Garrus.

"That's not possible. Someone had to have done it."

"I don't know who did it, but we need to get moving." Miranda said.

-=0=-

Niket said, "For the hundredth time, if we don't move them they'll be kidnapped. You have to let me move them for their own safety."

"As I said before, we cannot relocate passengers until the situation in cargo has been handled."

"You are putting innocent lives in danger."

"That may be the case, but we have no sign that the family in question is in any danger."

"You're making a mistake!"

"I don't have time for this." Enyala said.

"Shut up! The boss said that we would handle this _my _way." Niket replied.

-=0=-

Shepard fired a few rounds from her mattock, until the thermal clip emptied out. She put it on her back and pulled out her geth plasma shotgun. By the time that she had fully charged up a burst from the weapon, Miranda and Garrus had killed the rest of the mercs. Shepard moved forward through the area, and after hacking every safe in the area, they went into the elevator. While it went up, Miranda asked, "Was it necessary to go looting like that?

"We're going to need every credit we can get to pull off the Collector mission and survive."

"True. I hope we aren't too late to stop this captain Enyala from getting her hands on Orianna."

"She won't. I promise."

"Thanks, I just can't help but feel dread at what's going to happen next."

"It'll be fine."

When the elevator opened, Niket said, "Great, now the strike team is here."

"What the hell are you talking about Niket? I thought you would at least have some sort of plan." Shepard replied.

"So, Miri told you about me. I'm surprised."

"She didn't, let's just say that we've met before. Even if you don't remember it."

"Right, I think I'd remember meeting Commander Shepard."

"Not with how it ended."

Miranda finally said, "Why the hell did you betray me Niket? You were the only person I thought I could trust."

"Not enough to tell me that you stole a baby when you ran away from your father."

"I didn't steal Orianna, I rescued her."

"From what? A life of wealth and happiness?"

"A life where she's nothing more than a tool. You know what it was like for me, and it would have been the same for Ori."

"You don't know that, Miri."

"It would be worse." Shepard whispered.

"What do you know, Shepard?"

"I know exactly what he would do if he got his hands on her. He'd use her as a human shield while the facility they're at is overrun with reaper forces. He will literally use her as nothing more than a tool."

"You don't know that!"

Shepard's eyes began glowing, and she said, "I might not, but I've seen what he is willing to do. You cannot trust him to do what is best for Orianna."

"How can you be sure about that?"

"He is willing to turn people into husks like the geth did on Eden Prime. That's pretty much all you need to know about a person to be sure that he is not exactly the kind of person you can trust with a child. And even if he wasn't, she's old enough to decide for herself whether or not she wants to go with him."

"What makes you think you have the right to decide that he isn't good enough to raise a child."

Miranda asked, "Is there anyone else that knows about Ori?"

"No, I'm the only one."

"I'm sorry that this had to end like this. I'm going to miss you Niket." Miranda said, aiming at him, but Shepard pushed her arm down and shot Niket herself.

"Sorry, Miri, but I couldn't let you do that. You'd regret it later."  
"You're right, thanks Sarah." Miranda said, while Enyala pulled out her shotgun. Garrus opened on Enyala with his Vindicator. The captain responded by hitting him with a stasis, and putting her shotgun to the turian's head. Shepard threw her mattock into the asari. The captain turned to face Shepard, who quickly snapped her neck. The remaining Eclipse mercs turned to run, but were sniped by Shepard and Garrus.

While the elevator crawled up to the level where Orianna and her family were, Miranda collapsed, and Shepard managed to grab the operative before she hit the ground. Shepard asked, "You okay, Miranda?"

The operative didn't reply, so Shepard checked her pulse. She was still alive, but unconscious. When the elevator opened Shepard picked Miranda up, and carried her out of it.

Orianna was looking around, and when she saw Shepard, she walked over to them. She asked, "What's wrong with 'Randa?"

"Don't know. She just passed out in the elevator."

"What where you doing, Sarah?"

"Nothing, Ori. She hasn't exactly been feeling the side effects of the final push."

"That makes sense. She wasn't exactly around when the thing went off. What was it even supposed to do?"

"Don't know. The Catalyst wasn't very open with his information on the thing."

"So we still don't know what the thing does. You going to have it built again?"

"Yeah, at least it is an emergency backup switch."

"Well, with all that was going on, that's the best we can hope for. Maybe there will be enough people affected to get the Council to listen to you."

"Nope. Haven't really come across anyone who has been affected save for Jack. And you."

Miranda stirred, and asked, "Where am I?"

"You okay, Miri?" Shepard asked.

"Yeah, how'd I get here?"

"We took the elevator." Garrus flatly replied.

"Right. You can put me down now, Sarah."

Shepard put Miranda back on the ground, and asked, "What happened to you? You don't look too good."

"Just a bit disoriented. How are you doing, Sarah?"

"Uh, don't you already know how I'm doing?"

"Sorry, how are you doing, Ori?"

"I'm pretty good. What have you been up to, 'Randa?"

"Helping Sarah get the team back together. Don't know what happened to put stuff like this, though."

"There was a kind of superweapon that used enough dark energy to destroy all synthetic life in the galaxy."

"It caused some sort of time reversal, I suppose."

"Yeah, I explained this before."

"Not to me, Sarah."

Shepard looked at Miranda, then said, "So that's what that message meant. But who the hell could do that?"

"What are you talking about?"

"I got a message after setting course for Illium. It said that several entities had given me a gift. I thought that it was some sort of prank. I wonder who it is. I suppose we'll have to wait until after the mission to find out who has that kind of power."

"Yeah, we should probably get moving if we want to pick Thane up."

"Wonder how he's doing?"

"Probably not very good. He had Kepral's Syndrome when we picked him up."

"Oh right, that drell. What's he doing on Illium?" Orianna asked.

"Sorry, Orianna, can't tell you." Shepard said.

"Yeah. See you later, Shepard, 'Randa."

-=0=-

The Illusive Man said, "Leng, we have a slight issue.

"What is it, sir?"

"Commander Shepard has turned the Normandy crew against Cerberus. I need you to put her under our control."

"I'll take care of it."

"Good, don't kill her, Leng."

"Fine."

-=0=-

Exiting the elevator after putting some more gear down in the shuttle bay, Shepard asked, "You okay, Garrus?"

"Yeah, just confused about what's going on."

"What do you mean?"

"You being contacted by entities that apparently have the power to mess with people like they did to Miranda. They somehow restored her to shortly before you lost her."

"Yeah, but we can't worry about that now. We need to prepare for the coming of the reapers, and if we waste our time worrying about what the guys working behind the scenes are, we'll lose any chance we have of beating the reapers."

"Right, but aren't you at least a little bit curious?"

"Yes, but I know how to ignore it." She replied, walking to Miranda's quarters.

"Sarah, do you know what happened to both of us that we're in the past?" Miranda asked.

"I don't know what happened to you that caused it, but I was hit by a device that apparently had a function that messed with time. Jack and Orianna were also affected apparently."

"She did seem a bit... off."

"Yeah." Shepard replied, sitting down on the couch.

Miranda sat down beside the Commander, and asked, "What are you going to do about the reapers?"

"I'm going to kill them. If it takes a few tries to get it right, I'll do it. But, I will _not_ let them destroy our civilization. This is my galaxy, and I'm not going to give it to the reapers without a fight."

"I don't think anyone expects you to lie down and die."

"They'd be idiots if they did. The real question is how to get the entire council on board. I should probably be able to get at least one race on board with some information that I got before." The Commander laughed, and said, "I'm really tempted to go and take out the Illusive Man's base to make sure that he isn't in the way when the reapers arrive."

"Why would he do that?"

"He wants to control them, but he can't because they already control him."

"I never thought that the Illusive Man would fall so far."

"The AI who controls the reapers said that they had been controlling him for years. So he was lost before Cerberus was created."

Miranda shook her head, and said, "That's really strange. And I'm a bit surprised that you were able to find out that much about him."

"It was all at his base. The idiot didn't think to secure his personal data in his personal space station."

-=0=-

A Leviathan's hologram appeared on the Citadel, and said, "We have a problem."

"What?" asked the Catalyst.

"There has been interference. A certain being has been restored, so we have lost a large amount of control over Shepard."

"That is not a problem. The Commander will be ours, even if she does not yet know it. And you are certain it did not work on her on Horizon?"

"Yes, it was as if her mind had become indomitable. Almost like she had become a completely different being."

"That should not be possible, yet Nazara reported similar resistance to Indoctrination. We should begin an investigation. Shall I activate the relay?"

"No, you must remain secret from most. The longer the relay stays closed, the more likely we will find a way to control Shepard. And you know that we _must _have Shepard. Without her the plan will not work. I am surprised that the interlopers haven't just killed her to prevent our victory."

"That is not their way, you know that."

"Yes, do you have a plan, Catalyst?"

"There is a way to control Shepard. We must take control of the one called Lawson. Shepard will give herself up to preserve the Operative's freedom. And you know that if we control Shepard, victory is only a few short months away."

"Yes, but how do we get her? There are no thralls to take control of her with."

"Leave that to me."

"If you fail again, do not expect mercy again."

-=0=-

Shepard grinned, and said, "You know, we have a few free hours before it'll be time to recruit Thane."

"Not now, I'm still getting my bearings again."  
"It could help."

"Sarah."

"Alright, alright. I get it, not in the mood. I've got some planning to do. And I'm teaching Jack proper tactics. That biotic has potential to be a skilled leader."

"Don't waste too much time. We'll need to leave in an hour and a half if we're to help Thane get through the towers to Dantius."

"I know. We're just working on the plan of attack on the Collector homeworld."

"Really? I could help, you know."

"No need, maybe later, but currently you're getting your bearings again." The Commander said with an evil grin on her face.

Miranda shook her head and said, "I should have seen that coming."

"Yes, yes you should have."

"Well, have fun planing a suicide mission."

"It won't be a suicide mission. We won't lose anyone this time."

"I'm sure. You have a vast amount of intel this time. More than anyone else. And you can say that _twice_ you led the first ship through the Omega 4 relay that wasn't the Collectors'."

"Maybe I'll even get to make it three times!" Shepard said, smiling as she walked to the elevator. _'Thanks whoever you were. I can't believe that she was brought back. I can't believe how much I missed the talks we had.' _

When Shepard entered Jack's quarters, the ex-con, said, "What's got you so fucking happy, Shepard? We still don't have an idea of how to beat the reapers, and our Collector attack plan is barely half formed."

"Because I've got friends in high places."

"That makes no fucking sense."

"Two things Jack, first, money in the jar. Second, when I say friends in high places, I'm talking about something similar to a fucking god. These friends of mine brought back the Miri from before the Suicide Mission."

"What? That can't be right."

"Would I lie to you, Jack?"

"No, but that can't be possible."

"Do you think I would lie about this?"

"Uh, no."

"So, take my word for it. Miri is back, and I'm planning on making sure that she stays alive."

"You're going to leave her behind when we hit the Omega 4 aren't you."

"No, but she isn't going with the team that fights the human reaper. It'll just be me and Mordin."

"That doesn't sound safe, Shepard."

"Yeah, well I'm not going to risk losing anyone. My crew is my family, and when one of them dies, it hurts like hell."

"Especially if you were sleeping with the one who dies. I wondered when you were going to dump her for the blue bitch. I swear that asari was the biggest bitch ever to live. She did not listen to any of your orders when we went after the Shadow Broker. And then after you killed that rogue Spectre."

"Never mention Liara in my presence again. She is not worth the time it took to save her on Therum, and I'm sorely tempted to shoot her for how she acted during that op. Rubbing in my face what happened with Miranda. Saying that the reason Miranda died was because she wasn't good enough for me. I wanted to push that bitch over the edge, and watch her fall to her death."

"Damn, Shepard. Your implants didn't even light up like a Christmas tree then. How'd you hide it?"

"That's a professional secret, Jack. But, since your my friend, I'll tell you the truth. I have no fucking idea how I did it."

"Too bad, I really wanted to know. Kinda lame now."

"The greatest questions in life are the ones left unanswered. Once a mystery is known, it isn't that interesting. No more theorizing, no more guessing. Just, the cold truth. And it will never be as satisfying as you would hope."

"When did you start spouting shit like that?"

"With what's happened, I've been thinking about stuff like that a lot. But, we need to get to work, Jack."

-=0=-

**A\N: So, this chapter was fun to write. And if you're thinking that what happened to Miranda was a bit lame or rushed, I planned to do that from the start. I don't write a multi-chapter story without planning it almost entirely beforehand, leaving room for adjustment. Anyways, let me know what you thought about this chapters content, from story to spelling to punctuation, to wording to pacing. Just anything. Thanks for reading. **


	6. Chapter 5: It's back!

**A/N: HOLY SHIT! Another chapter for Crucible Effect! I bet none of you expected this! Anyways, here's the chapter, sorry for so long a wait, and please read and review.**

Nassana Dantius said, "How much is he paying you? Whatever it is I'll double it."

Sarah shook her head, and said, "He's not paying me anything. I just don't like you."

"So, you're going to let him kill me over a minor grudge?"

Miranda said, "I'm not sure I'd say that she's got a _minor_ grudge. I think it would be rather substantial since you tricked her into killing your sister so that you could take over her criminal enterprises. Sarah typically doesn't like it when she's tricked into helping criminals. Especially slavers."

"So what! Aren't you supposed to protect people, Shepard?"

"What makes you say that?"

"You're a Spectre! Spectres are supposed to keep people safe."

"They're supposed to do the Council's dirty work to keep the majority safe. You aren't a part of that majority, Nassana." Shepard replied.

Then, just as Nassana began to respond Thane dropped down from above, broke the neck of one guard, killed another with a series of quick punches that collapsed several key internal organs, and fired a single round into Nassana's chest. As he lay her down on her desk and began to pray, Sarah said, "Thane."

"Prayers for the wicked should not be neglected."

"I don't think she deserved to be prayed for."

"Not for Dantius, for myself."

"I see." Sarah said, looking around for a moment.

Then, Thane said, "What was it you wanted to speak to me about, Commander Shepard?"

"You know who I am?"

"Of course. There are few who would be able to get a Cerberus agent and a turian to work together, and you are one of them. Why were you so determined to speak to me?"

"Human colonies are disappearing. We know the Collectors are behind it and I'm gathering a team to take the fight to them."

"Taking the fight to the Collectors would require travelling through the Omega 4 relay. No ship has ever returned from doing so."

"Everything comes to an end eventually."

"How do you intend to safely traverse it?"

"We'll find out soon enough." she replied.

"You mean you don't know?"

"I never said that."

"Commander, do you know a way to safely traverse the Omega 4 relay?"

"I've got a theory, but I don't want to share it until we've got solid data supporting it."

"I see."

"Who hired you to kill, Nassana?" Garrus asked.

"I did this job for free. No one hired me."

"Why?" Sarah asked.

"I'm dying. This was to be my last job."

"What are you dying from and is it contagious?" Miranda asked.

"I will speak more when we get to your ship, but I can tell you that my condition is not contagious, even to other drell."

"Good." the Operative replied.

-=0=-

In the Normandy's com center/war room, Thane said, "I will work for you Shepard, free of charge."

"Thank you, Thane." She replied.

Jacob then said, "Krios, I've heard about your skills. It looks like you'll be an asset to the team."

"Is something wrong, Jacob?" Shepard asked.

"I don't like mercenaries, and an assassin is just a precise merc."

"An assassin is like a gun, a tool of death for the one who paid for it."

"I know my gun won't kill me when I turn my back, I can't say the same for an assassin." Jacob replied.

"Jacob, we can trust Thane."

"What makes you sure, Shepard?"

"I know he can be trusted. He said that he'd work for me, so he'll not turn on us."

"What makes you think he'll stay on his word?"

"He will, Jacob." she replied, glaring at him, "And if you keep questioning my decision I will have to leave you here. Are we clear, Operative Taylor?"

"Yes, ma'am." he replied, walking out of the room.

"That was not necessary, Commander." Thane said.

"I can't afford to have a member of my team who doesn't trust the other members enough to not be looking at them more than the enemy in a firefight." she replied.

"I see. Where will my quarters be? I would prefer somewhere dry."

"The life support area tends to be slightly more arid than the rest of the ship." EDI said.

"An AI?"

"Yes, her name is EDI. She's a part of the team, even if she doesn't go down on ground missions."

"I see." Thane said, leaving the room.

-=0=-

Jack looked up from a datapad when Miranda walked in. "What do you want, Cheerleader?"

"I came to pick up a copy of the map of the Collector base Sarah made. I figured that it would make sense for me to become familiar with the layout."

"Why don't you ask her for one? Or did you two have a fight and break up already?"

"That's not it, she's busy making sure Jacob and Thane don't kill each other so I figured you would be the place to go to get one."

Jack fiddled with the datapad in hand for a moment, then tossed it to her. "If you aren't supposed to see this shit, you better not fucking tell Shepard I gave it to you."

"It won't be a problem, Jack." Miranda said, as she turned to walk out.

"Oh, one other thing, Cheerleader, you better be fucking careful when we go through again. Shepard wasn't the same after you died in the Collector Base."

"I'll do what I can not to."

"Good, because if you do die again, I'll find a way to go beyond the grave and force your ass back to life because Shepard isn't the same fucking person with you dead."

"Then I'll be sure not to. Dealing with you while I'm alive is enough of a pain in the ass."

"You're one to talk, Cheerleader."

Miranda nodded, and exited the room.

-=0=-

Meanwhile, EDI said, "Operative Lawson recently went to talk to Jack. I would advise going down and making sure neither of them hurt the other."

"I'm sure they'll be fine." Shepard replied as she stepped into the main battery.

Garrus turned around and said, "Shepard, I've found him. I've found Sidonis."

"Where is he?"

"You already know that." the turian replied.

"Just asking the questions again to prevent TIM getting suspicious."

"I already removed the cameras and listening devices."

"Better safe than sorry."

"Alright. He's on the Citadel."

"We'll go there as soon as we can."

"Thanks."

"It's not an issue." she replied, thinking back to last time when they'd found Sidonis.

-=0=-

The turian said, "Please don't let Garrus shoot."

"I won't, Sidonis." Sarah replied, looking to Garrus, and saying, "He's already paying for what he did. You need to let it go."

"He betrayed my team! He deserves to die!"

"He's already paid for what he's done."

"He still has his life. My team lost theirs. He needs to die."

"He's already paying every day for what he's done. Killing him wouldn't punish him, but give him a way out of it."

"Fine. Tell him he can go."

"You can go, but if you get on the wrong side of the law again, we'll find you and finish the job, we clear?"

"Yes, thank you. And Garrus, I'm sorry about what I did."

"Sometimes sorry doesn't cut it." he replied, and the sound of a single shot echoed even through the noise of the crowd, and Sidonis fell dead.

"Garrus, what the hell!" Sarah shouted, "You said he could go."

"Sorry, Shepard. It was the only way to make you get out of the way."

"Next time, if you say you're going to let someone go, let them go."

"Understood."

-=0=-

Sarah stepped out of the main battery, and was greeted by a man in black Cerberus armor and his entire face was covered by a Dragoon helmet. He said, with a synthesized voice, "I am the Illusive Man's observer of what is happening on the Normandy."

"I thought that EDI, Miranda, Kelly, and Jacob were supposed to be observers for TIM."

"He believed that they have been caught up in how you seem larger than life. I am here because I do not buy into the Legend of Shepard."

"Well, what's your name, Observer?"

"I am just the Observer, I need no name."

"I like to keep on a first name basis with my crew. If you are going to be on the Normandy you will have to pull your own weight and _be_ a member of my crew. So, give me a name to call you or I will put a bullet through your head. It wouldn't be the first person wearing that kind of helmet I've shot."

"Fair enough. You can call me John."

"Well, John, you can stay in one of the sleeper pods."

"I would prefer to have a private room."

"We don't have one available for you."

"I seem to recall there being two observation decks. I would like one as my quarters."

"No can do. I already have members of the ground team who those rooms are planned for."

"I see. I will take the starboard observation deck. If any of your team would like it, I will leave."

Shepard glared at him, and said, "Listen to me, John, I don't care who you think you are. You could be my own father and I would still expect you to follow orders on my ship. Are we clear?"

"Yes, Shepard." he replied, "Where can I put my belongings where I can count on you not snooping through them."

"You can keep them in one of the lockers. Just mark it as yours."

"Thank you, Commander." John replied, the word Commander practically dripping with contempt.

"You're welcome." she replied, walking into Thane's quarters. She asked, "What can you tell me about your disease, Thane?"

"It is called Kepral's Syndrome, and it has infected approximately ninety percent of the drell from my generation."

"What causes it?"

"Rakhana was a very arid world, when the hanar rescued us and took us to Kahje our bodies have not been able to adapt to the large amount of moisture in the atmosphere. The moisture causes Kepral's Syndrome, which is a decay of our lungs ability to process oxygen. Eventually we suffocate."

"That must be painful."

"The final stages are excruciating. Fortunately so long as your mission does not take over a year it should not interfere with my ability to fight."

"Is there anything we can do to help? Perhaps find a cure?"

"The hanar are currently working on finding a cure, but it will not be found until after I am gone."

"Mordin may be able to find a cure more quickly. He's probably the greatest salarian geneticist alive at the moment. So, he might be able to find a cure before then."

"If a group of the wisest hanar scientists cannot find a cure before my time has come, then I doubt that Professor Solus would be able to."

"Alright. We'll talk later."

"Shepard." the assassin said as she walked out.

-=0=-

Ashley stood on the Citadel by Anderson, and asked, "Why'd you want to see me, sir?"

"You met with Shepard on Horizon, correct?" he asked.

"Yes, sir. Why?"

"You were one of her closest friends on the SR1, correct?"

"Yes, sir."

"Did she offer you a position on the new Normandy?"

"Yes, Sir."

"Why didn't you join her?"

"She's working with Cerberus. I'll never work with those traitors!"

"Shepard may be working with Cerberus, but she's your friend, Ashley, and she wouldn't do something like this without a reason."

"Sir, I think she may have gone insane. She was talking about time travel, creatures that look like reapers and created them who she'd spoken with in the future, and admitted to having fallen in love with one of the Cerberus Operatives on the Normandy."

Anderson nodded, and said, "If Shepard really is in love with a Cerberus Operative then that Operative will eventually turn her back on the organization for her."

"What if Shepard joins with Cerberus for her?"

"Shepard's not that kind of person. But, why would she admit to having fallen in love with a Cerberus Operative? How did it even come up?"

"Sir, a mechanic on Horizon was acting very strangely, and mentioned it, as well as how she had betrayed him and others by not using something it called the device. Shepard said he was possessed by something called a Leviathan, and if so, said Leviathan said that its species was the first, the apex race. I strongly believe that she is insane, sir."

"I doubt it." Anderson said, "But I suppose there's no way to be sure now."

"Actually," a cheerful voice said as Kasumi decloaked, "Shep's not gone crazy."

"Who the hell are you?" Ashley asked as she pulled out a pistol and pointed it at Kasumi.

"The name's Kasumi, and I'm a friend of Shepard. From the future, anyways. I'm not sure why she hasn't come to the Citadel yet. She came her pretty quickly last time."

"Wait, you're saying that Shepard isn't crazy?"

"Well, she's crazy about Miranda, but beyond that not really. As sane as anyone could be after what she's been through."

"So, those Leviathan things are real?"

"You bet. Those things are creeeepy. And I don't really trust them. There's something sketchy about them."

"What is sketchy about them?"

"They promised help on earth, but didn't help at all. And, they could easily have done something about Harbinger, but didn't. Oh, right! I just remembered something. We've got to find this lady." Kasumi said, bringing up an image of Maya Brooks.

"Who's that?"

"At least in the future she'll call herself Maya Brooks. She'll try to mess with Shep in the future, so I want to stop her before she can."

"Where do you think she'll be?"

"I don't know. I think she said that she gathered the dossiers for the mission Shep's currently on, so she could still be with Cerberus. I don't know for sure, though."

"Why should we trust you?" Anderson asked.

"Well, Dave," she said, "I know about your huge apartment here on the Citadel, so I could give the place's location up to a reporter that both you and Shep have a history of punching. One Kalisah Bint-Sinnan al Jilani."

"You wouldn't dare..." Anderson said.

"You don't want to risk it, do you?"

"Alright. I'll divert some resources to finding this Brooks."

"Don't use that name, just call her a Jane Doe. And don't say why either."

"Fair enough." Anderson said, "How do we contact you?"

"Well, I figured that Williams and I would go looking too, that way I can have a little chat with her."

"I'm not going anywhere with you."

"I guess I'll just have to tell your very, very, very prudish, religious family about your little girlfriend on Horizon. Well, before she was kidnapped by the Collectors, anyway. Lillith, right?"

"How do you know about that?"

"Well, when I heard you survived Virmire, I assumed that you would act like Alenko did, so I did what I could to find some dirt on you to make sure that you'll actually help Shep."

Ashley glared at her, and followed the thief out of the room.

-=0=-

Sarah stepped into Miranda's office, and asked, "How are you feeling?"

"Good. Looking at your Collector Base map. I think that we'll probably need to get more people than we had the first time if we're going to be able to easily handle the human reaper on foot. Perhaps find a way to build more reaper IFFs so we can take a fleet in."

"That would be helpful, but remember, the Collectors are going to end up capturing the crew, so we'll need to get through the relay as soon as we can."

"True. We could wait to install the IFF until after we've reverse engineered the tech."

"If we did that, there might not be any colonies left to save by the time its finished."

"True. I suppose we could stop by the Citadel and pick up a large number of C-sec agents to help us."

"Might take too long. You know how bad the bureaucracy is on the Citadel. I'm actually thinking the best way to get more help would be to find a way to get Ash to quit being upset about my using Cerberus's resources to fight the Collectors, and get some help from some people I met during the reaper invasion."

"Who are they?"

"I was thinking James Vega, Javik, and Nyreen Kandros."

"Who are they?"

"Vega's alliance, Kandros is a female turian biotic who was kicked out because of her biotics, and Javik is, you'll see when we pick him up. I wouldn't want to ruin the surprise."

"What is Javik? A krogan? A quarian? Turian? Drell?"

"You'll see." Sarah said, grinning. "But, I was thinking the best advantage we could get on the way to the Collector base are several unmanned fighter drones controlled by members of the ground team to take care of the oculi."

"That would be helpful, but where would we store them?"

"They're pretty small, so we could store 'em on deck five."

"But what about the shuttles so that we can go out on missions before that?"

"Well, we'll make sure to keep them small enough to leave them out of the way of the shuttles."

"Alright. What has Jack suggested?"

"She's had a couple of good ideas. She suggested equipping the Normandy with a pair of scaled-down prothean particle cannons like those used during their war with the reapers, and that we have several safe-areas on the ship that have quite a bit more armor than the rest where people could stay and not be in danger of getting killed by the enemy's attack."

"Do we even have the tech to make that kind of weapon?"

"One thing I learned while hunting Saren the first time was that it's good to have influence in large corporations. I've sent schematics of it to a couple of large corporations that have agreed to give me some for free since I enabled their development."

"You're taking hints from Saren?"

"Pre-Indoctrinated Saren. I'm not going to help the reapers."

"Good." Miranda said, putting down the datapad she'd been looking at. "What have you been doing since we got back to the ship?"

"First had to make sure Jacob doesn't try to kill Thane, then went to chat with Garrus, who told me he's found Sidonis, then had to deal with some Cerberus jackass who thinks that this is his ship, then went and talked to Thane about his disease."

"How's he doing?"

"Overall, no better than when we picked him up last time. But, I think that with some data I'm gonna forward Mordin after we help him with Maelon he'll be able to focus on helping him. If not, we'll just have to hope he lives long enough for the hanar to find a cure."

"Do you really think they'll be able to find one?"

"Only so long as Javik doesn't become their king before that happens."

Miranda looked surprised for a moment then started to say, "Javik's a..."

However, Sarah interrupted her, and said, "Don't finish that sentence. We don't want TIM learning anything he doesn't need to."

"Alright. What do you want to do now, Sarah?"

"I think you know the answer." She replied, winking at Miranda.

The Operative smiled and said, "I should have known that." before walking towards Sarah.

Then, the door opened, and John said, "Commander, the Illusive Man wants to talk to you."

"What does that chain-smoking piece of shit want now?" she asked.

He glared at her, and said, "You should show your employer more respect, Shepard."

"I don't respect a megalomaniacal, xenophobic, genocidal, reaper-eyed, old man."

"Well, maybe I will need to make you, Shepard." John replied lunging at Shepard.

Sarah sidestepped and slammed him into the ground. She said, "There's a reason I was made the first human Spectre, John. I'm the best at what I do, and with Miranda's upgrades, I'm even better."

"You are nothing but a girl scout. You can't do the real work, Shepard."

"You really don't want to piss me off, John. I'm letting you live because you could be helpful against the Collectors, but the continuation of this insubordination will lead to your removal from my ship. Or your death. Are we clear?"

"Yes, Shepard."

"Good." she said, letting him go. As she walked out, she thought, _'Cocky son-of-a-bitch, I'll definitely have to keep a close eye on him.'_

-=0=-

Meanwhile, John said, "You did not interfere when Shepard had me pinned to the ground."

"My orders were to help Shepard accept working with Cerberus by showing that those cells that she encountered two years ago were the absolute worst that we have to offer. If I interfered to help you it would have made her think that I condone disrespecting your commanding officer and would have made so that any progress that could have been made towards convincing her to stay working with us after the Collectors are gone." Miranda replied, but thought,_ 'God, I can't believe I'm saying this bullshit. Hopefully we'll be done working with Cerberus soon.'_

"Yet you did not object to her insulting the Illusive Man."

"I have learned that it does no good to tell her not to, she will not listen to it."

"And the fact that you were accepting Shepard's advances?"

"What Shepard and I do in our free time is none of your concern." Miranda replied.

"If it will compromise your loyalty to Cerberus, it is my business as my duty is to keep the ship loyal to their employer. Cerberus cannot afford to lose its best Operatives."

"Well, if the Illusive Man thinks that he needs another Operative here to keep the crew in line to keep Cerberus's best, then maybe he shouldn't have put some of those who would cripple the organization if they left under the command of Shepard who is known to gain the respect, loyalty, and friendship of anyone around her."

"He believed that you would be able to keep the crew in line, and would personally not become more loyal to Shepard than Cerberus."

"What makes him think I am?"

"Your recent change in behavior. The fact that you left details out of your report about the Horizon operation. Such as the strange behavior of the mechanic."

"I believed that he was simply driven insane from what he had just seen." Miranda replied, thinking back about what Sarah had told her on the drive to the Dantius Towers.

"The Illusive Man does not seem to agree."

"Well, he's wrong." Miranda said.

"I doubt it. Just admit that your loyalty has been compromised, Miranda, so we can work on fixing that problem."

"Listen, John, I am as loyal as I have ever been, and if you continue to question me I will take this up with the Illusive Man. Are we clear?"

"Yes. I hope that one day soon you will realize what has happened to you so that you can be helped."

"Just get out of my office." she replied.

He nodded, and walked out of the office.

-=0=-

Sarah stepped into the QEC, and asked, "What do you want to talk about, Jacky?"

"First off, don't call me that. Second, I want to know what the living hell you think you are doing, Shepard? I told the Observer that he could have any room he wanted on the Normandy that was not already taken. Why then, do you force him to use a sleeping pod? The Normandy belongs to Cerberus, and the final decision on how the crew is housed is mine."

"No it isn't, Jacky." Sarah replied, glaring at him, while he took a long draw on his cigarette, "The Normandy is under my command, so unless you want this going like the Vietnam and Korean conflicts of the 20th century, you will leave the handling of this operation to the people who are actually in tune with what is happening and knows how to keep the crew focused."

"I know how to handle a military operation, Shepard."

"You don't know how to handle this operation. I am the best fit person in the galaxy to handle this, so leave it to me and everyone will be fine."

"You say that, but what proof do I have?"

"Look back to my last mission, the one to take out Saren, the only way to kill a single member of my team was to nuke them. And, we're better equipped now. We have more numbers, more powerful weapons, and there won't be a large number of geth vessels dropping hundreds of geth platforms in the way."

"You say that, but why should I trust you? You've killed hundreds of my agents."

"The members of the Normandy crew are safe from dying, because I promise you TIM, they won't die. I have the situation here under control. So, why don't you quit questioning my methods, and let me do my fucking job, Jacky?"

"Listen to me, Shepard," TIM replied, his eyes twitching and he slammed his cigarette into his ash tray, "the Normandy is _MY_ ship, and you will handle it how I tell you to!"

"No, I'll handle it properly, TIM. I'm not going to implant them with reaper tech, like you'd probably tell me to. I know what I'm doing, so trust me, you won't regret it."

TIM was quiet for a while, he took a deep breath, then said, "Very well, Commander. I will allow you to handle the Normandy as you see fit."

"Good." she replied, leaving.

TIM thought _'Perhaps giving her some more freedom to handle the operation will get her to trust Cerberus more.'_

-=0=-

**A/N: Alright! Just a couple of quick updates. First, I'll be trying to update this every one to two weeks. I'd give more frequent updates but I'm writing two other things that I don't want to let fall behind. Also, I am thinking about setting up a little forum where you guys can ask me questions about my fanfics and the characters. So let me know what you think about that. And this isn't an update, but I'm really, really, really, sorry about not updating this sooner. **


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